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Tao Liu - Publications

Affiliations: 
Department of Biochemistry State University of New York, Buffalo, Buffalo, NY, United States 
 Oncology Roswell Park Comprehensive Cancer Center 
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Niu S, Li J, Bo W, Yang W, Zuccolo A, Giacomello S, Chen X, Han F, Yang J, Song Y, Nie Y, Zhou B, Wang P, Zuo Q, Zhang H, ... ... Liu T, et al. The Chinese pine genome and methylome unveil key features of conifer evolution. Cell. PMID 34965378 DOI: 10.1016/j.cell.2021.12.006  0.341
2020 Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer CA, Brown M, Tang M, Long H, Liu T, et al. Integrative analyses of single-cell transcriptome and regulome using MAESTRO. Genome Biology. 21: 198. PMID 32767996 DOI: 10.1186/S13059-020-02116-X  0.392
2019 Tarbell ED, Liu T. HMMRATAC: a Hidden Markov ModeleR for ATAC-seq. Nucleic Acids Research. PMID 31199868 DOI: 10.1093/Nar/Gkz533  0.374
2017 Zhang P, He D, Xu Y, Hou J, Pan BF, Wang Y, Liu T, Davis CM, Ehli EA, Tan L, Zhou F, Hu J, Yu Y, Chen X, Nguyen TM, et al. Genome-wide identification and differential analysis of translational initiation. Nature Communications. 8: 1749. PMID 29170441 DOI: 10.1038/S41467-017-01981-8  0.528
2016 Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XS. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Research. PMID 27789702 DOI: 10.1093/Nar/Gkw983  0.711
2016 Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, et al. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. Bmc Bioinformatics. 17: 404. PMID 27716038 DOI: 10.1186/S12859-016-1274-4  0.696
2014 Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415  0.608
2014 Meijer DH, Sun Y, Liu T, Kane MF, Alberta JA, Adelmant G, Kupp R, Marto JA, Rowitch DH, Nakatani Y, Stiles CD, Mehta S. An amino terminal phosphorylation motif regulates intranuclear compartmentalization of Olig2 in neural progenitor cells. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 34: 8507-18. PMID 24948806 DOI: 10.1523/Jneurosci.0309-14.2014  0.323
2014 Liu T. Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells. Methods in Molecular Biology (Clifton, N.J.). 1150: 81-95. PMID 24743991 DOI: 10.1007/978-1-4939-0512-6_4  0.382
2013 Shin H, Liu T, Duan X, Zhang Y, Liu XS. Computational methodology for ChIP-seq analysis. Quantitative Biology. 1: 54-70. PMID 25741452 DOI: 10.1007/s40484-013-0006-2  0.604
2013 Catic A, Suh CY, Hill CT, Daheron L, Henkel T, Orford KW, Dombkowski DM, Liu T, Liu XS, Scadden DT. Genome-wide Map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation Cell. 155: 1380-1395. PMID 24315104 DOI: 10.1016/J.Cell.2013.11.016  0.608
2013 Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J. Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data Plos Computational Biology. 9. PMID 24244136 DOI: 10.1371/Journal.Pcbi.1003326  0.408
2013 Sun H, Qin B, Liu T, Wang Q, Liu J, Wang J, Lin X, Yang Y, Taing L, Rao PK, Brown M, Zhang Y, Long HW, Liu XS. CistromeFinder for ChIP-seq and DNase-seq data reuse. Bioinformatics (Oxford, England). 29: 1352-4. PMID 23508969 DOI: 10.1093/Bioinformatics/Btt135  0.629
2013 Xu K, Wu ZJ, Groner AC, He HH, Cai C, Stack EC, Loda M, Liu T, Morrissey C, Vessella RL, Kantoff PW, Balk SP, Liu XS, Brown M. Polycomb-independent activity of EZH2 in castration resistant prostate cancer Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-O14  0.569
2012 Xu K, Wu ZJ, Groner AC, He HH, Cai C, Lis RT, Wu X, Stack EC, Loda M, Liu T, Xu H, Cato L, Thornton JE, Gregory RI, Morrissey C, et al. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science (New York, N.Y.). 338: 1465-9. PMID 23239736 DOI: 10.1126/Science.1227604  0.619
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... ... Liu T, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  0.557
2012 Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using MACS. Nature Protocols. 7: 1728-40. PMID 22936215 DOI: 10.1038/Nprot.2012.101  0.63
2012 Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods. 9: 609-14. PMID 22522655 DOI: 10.1038/Nmeth.1985  0.672
2012 Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y, Liu XS. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics (Oxford, England). 28: 1411-2. PMID 22495751 DOI: 10.1093/Bioinformatics/Bts157  0.629
2011 Tang Q, Chen Y, Meyer C, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M, Liu XS. A comprehensive view of nuclear receptor cancer cistromes. Cancer Research. 71: 6940-7. PMID 21940749 DOI: 10.1158/0008-5472.Can-11-2091  0.661
2011 Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology. 12: R83. PMID 21859476 DOI: 10.1186/Gb-2011-12-8-R83  0.668
2011 Feng J, Liu T, Zhang Y. Using MACS to Identify Peaks from ChIP-Seq Data Current Protocols in Human Genetics. 34. PMID 21633945 DOI: 10.1002/0471250953.Bi0214S34  0.395
2011 Feng D, Liu T, Sun Z, Bugge A, Mullican SE, Alenghat T, Liu XS, Lazar MA. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science (New York, N.Y.). 331: 1315-9. PMID 21393543 DOI: 10.1126/Science.1198125  0.565
2011 Wang X, Laurie JD, Liu T, Wentz J, Liu XS. Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. Genomics. 97: 235-43. PMID 21295131 DOI: 10.1016/J.Ygeno.2011.01.006  0.55
2011 Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS. MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biology. 12: R11. PMID 21284836 DOI: 10.1186/Gb-2011-12-2-R11  0.657
2011 Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung MS, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P, Rosenbaum H, Shin H, Taing S, Takasaki T, Iniguez AL, et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Research. 21: 227-36. PMID 21177964 DOI: 10.1101/Gr.115519.110  0.349
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914  0.634
2009 Shin H, Liu T, Manrai AK, Liu XS. CEAS: cis-regulatory element annotation system. Bioinformatics (Oxford, England). 25: 2605-6. PMID 19689956 DOI: 10.1093/Bioinformatics/Btp479  0.62
2009 Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nature Genetics. 41: 376-81. PMID 19182803 DOI: 10.1038/Ng.322  0.605
2008 Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biology. 9: R137. PMID 18798982 DOI: 10.1186/Gb-2008-9-9-R137  0.411
2008 He S, Su H, Liu C, Skogerbø G, He H, He D, Zhu X, Liu T, Zhao Y, Chen R. MicroRNA-encoding long non-coding RNAs Bmc Genomics. 9: 236-236. PMID 18492288 DOI: 10.1186/1471-2164-9-236  0.312
2007 He S, Liu C, Skogerbø G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R. NONCODE v2.0: decoding the non-coding. Nucleic Acids Research. 36: 170-172. PMID 18000000 DOI: 10.1093/Nar/Gkm1011  0.325
2007 He H, Wang J, Liu T, Liu XS, Li T, Wang Y, Qian Z, Zheng H, Zhu X, Wu T, Shi B, Deng W, Zhou W, Skogerbø G, Chen R. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Research. 17: 1471-7. PMID 17785534 DOI: 10.1101/Gr.6611807  0.376
2006 He H, Cai L, Skogerbø G, Deng W, Liu T, Zhu X, Wang Y, Jia D, Zhang Z, Tao Y, Zeng H, Aftab MN, Cui Y, Liu G, Chen R. Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Research. 34: 2976-83. PMID 16738136 DOI: 10.1093/Nar/Gkl371  0.329
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